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BioC 2.14: CHECK report for DECIPHER on moscato2

This page was generated on 2014-10-08 08:54:17 -0700 (Wed, 08 Oct 2014).

Package 214/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 1.10.1
Erik Wright
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/DECIPHER
Last Changed Rev: 95053 / Revision: 95116
Last Changed Date: 2014-10-07 03:12:04 -0700 (Tue, 07 Oct 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.10.1
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.10.1.tar.gz >DECIPHER-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_1.10.1.tar.gz
StartedAt: 2014-10-08 00:26:16 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:30:56 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 280.7 seconds
RetCode: 0
Status:  OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.10.1.tar.gz >DECIPHER-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/DECIPHER.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DECIPHER' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.14-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbld/bbs-2.14-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64/DECIPHER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [52s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
DesignArray     18.81   0.20    3.97
Array2Matrix    15.49   0.06    3.77
TileSeqs        10.53   0.00   10.53
BrowseSequences  9.53   0.05    9.59
** running examples for arch 'x64' ... [56s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Array2Matrix    14.61   0.23    4.05
DesignArray     14.54   0.14    3.67
TileSeqs        12.91   0.03   12.93
BrowseSequences  9.53   0.05    9.59
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.

DECIPHER.Rcheck/00install.out:


install for i386

* installing *source* package 'DECIPHER' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:58:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
AlignProfiles.c: In function 'alignProfilesAA':
AlignProfiles.c:385:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
AlignProfiles.c:371:39: warning: unused variable 'S' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML':
ClusterML.c:397:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:214:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:195:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:128:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:124:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'makeConsensusAA':
ConsensusSequence.c:602:12: warning: unused variable 'X' [-Wunused-variable]
ConsensusSequence.c: In function 'consensusSequenceAA':
ConsensusSequence.c:931:22: warning: 'AAs[22]' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c:603:22: note: 'AAs[22]' was declared here
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
DesignProbes.c:58:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:37: note: 'lastCycle' was declared here
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:48: note: 'thisCycle' was declared here
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:226:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c EnumerateSequence.c -o EnumerateSequence.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatch':
MultiMatch.c:184:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'firstMatchUpper':
MultiMatch.c:215:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchLists':
MultiMatch.c:244:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrder':
MultiMatch.c:349:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrderDual':
MultiMatch.c:552:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchRanges':
MultiMatch.c:670:8: warning: statement with no effect [-Wunused-value]
MultiMatch.c:628:12: warning: unused variable 'k' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
NNLS.c: In function 'NNLS':
NNLS.c:49:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function 'terminalMismatch':
TerminalMismatch.c:40:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DesignProbes.o DistanceMatrix.o EnumerateSequence.o MultiMatch.o NNLS.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DECIPHER' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:58:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
AlignProfiles.c: In function 'alignProfilesAA':
AlignProfiles.c:385:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
AlignProfiles.c:371:39: warning: unused variable 'S' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML':
ClusterML.c:397:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:214:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:281:12: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:62: note: 'minC' was declared here
ClusterNJ.c:280:12: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: note: 'minR' was declared here
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:128:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:199:12: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: 'minC' was declared here
ClusterUPGMA.c:198:12: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: 'minR' was declared here
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'makeConsensusAA':
ConsensusSequence.c:602:12: warning: unused variable 'X' [-Wunused-variable]
ConsensusSequence.c: In function 'consensusSequenceAA':
ConsensusSequence.c:931:22: warning: 'AAs[22]' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c:603:22: note: 'AAs[22]' was declared here
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
DesignProbes.c:58:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:37: note: 'lastCycle' was declared here
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:48: note: 'thisCycle' was declared here
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:226:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c EnumerateSequence.c -o EnumerateSequence.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatch':
MultiMatch.c:184:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'firstMatchUpper':
MultiMatch.c:215:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchLists':
MultiMatch.c:244:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrder':
MultiMatch.c:349:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrderDual':
MultiMatch.c:552:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchRanges':
MultiMatch.c:670:8: warning: statement with no effect [-Wunused-value]
MultiMatch.c:628:12: warning: unused variable 'k' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
NNLS.c: In function 'NNLS':
NNLS.c:49:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function 'terminalMismatch':
TerminalMismatch.c:40:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DesignProbes.o DistanceMatrix.o EnumerateSequence.o MultiMatch.o NNLS.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_1.10.1.zip
* DONE (DECIPHER)

DECIPHER.Rcheck/examples_i386/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.540.013.87
AlignDB3.340.213.54
AlignProfiles1.340.011.36
AlignSeqs3.230.273.49
AlignTranslation1.650.061.72
Array2Matrix15.49 0.06 3.77
BrowseDB0.050.000.05
BrowseSequences9.530.059.59
CalculateEfficiencyArray0.050.000.05
CalculateEfficiencyFISH0.020.000.02
CalculateEfficiencyPCR0.030.000.03
ConsensusSequence0.010.000.01
CreateChimeras1.840.001.81
DB2Seqs0.040.000.03
DesignArray18.81 0.20 3.97
DesignPrimers000
DesignProbes000
DistanceMatrix000
FindChimeras0.460.000.47
FormGroups0.30.00.3
IdClusters0.030.000.03
IdConsensus1.620.031.65
IdLengths0.030.000.03
IdentifyByRank0.040.000.03
MODELS000
MaskAlignment1.170.061.22
NNLS000
RESTRICTION_ENZYMES0.000.020.02
SearchDB0.030.000.03
Seqs2DB0.530.000.53
TerminalChar0.010.000.01
TileSeqs10.53 0.0010.53
deltaGrules0.010.000.02

DECIPHER.Rcheck/examples_x64/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.640.020.65
AlignDB3.440.083.53
AlignProfiles1.380.031.40
AlignSeqs3.850.284.14
AlignTranslation2.030.032.06
Array2Matrix14.61 0.23 4.05
BrowseDB0.030.020.05
BrowseSequences9.530.059.59
CalculateEfficiencyArray0.020.000.03
CalculateEfficiencyFISH0.010.000.02
CalculateEfficiencyPCR0.020.000.01
ConsensusSequence0.020.000.02
CreateChimeras1.950.011.98
DB2Seqs0.030.000.03
DesignArray14.54 0.14 3.67
DesignPrimers000
DesignProbes0.010.000.01
DistanceMatrix000
FindChimeras0.610.000.61
FormGroups0.450.010.46
IdClusters0.030.000.04
IdConsensus1.750.001.74
IdLengths0.030.000.03
IdentifyByRank0.030.000.03
MODELS000
MaskAlignment1.380.051.41
NNLS0.010.002.76
RESTRICTION_ENZYMES000
SearchDB0.050.000.05
Seqs2DB0.610.020.62
TerminalChar0.040.000.05
TileSeqs12.91 0.0312.93
deltaGrules0.010.000.02